[IPT] IPT connection problem

Tue May 12 15:11:10 CEST 2009

Hi all,

> PS. I agree with Jörg that a convenient way to keep the old data  
> directory when upgrading the IPT would be cute.

This is indeed the case.  We will aim wherever possible to make  
upgrading as simple as it can be.
For bug fix releases, such as this snapshot, with no structural change  
the data directory can be migrated directly.   In future releases, we  
might require a "one time" migration task be run.  I anticipate the  
first one being required when the DwC standard is ratified.

> PPS. And a convinient way to add a thematic extension to the DwC  
> (for testing and demonstration) would also be very useful. I am  
> thinking of the draft DwC germplasm extension - as well as a new  
> draft for germplasm trait observation data I have started to work  
> on. I assume this perhaps could be done as an addition in the IPT  
> code somewhere around "WEB-INF/classes/org/gbif/provider/model/" ...?

A good suggestion.  We should look at setting up some sandbox  
repository for exactly this purpose.

Dag, for testing and demonstration you could do the following, but  
please be very careful not to register these datasets with GBIF.
- The IPT will call (http://gbrds.gbif.org/registry/ipt/ 
extensions.json and http://gbrds.gbif.org/registry/ipt/thesauri.json)  
to get the extensions and the thesauri.
- The response is fairly self explanatory, and for a test, you could  
override gbrds.gbif.org in you host file, and put up a different  
version locally for example referencing your test extensions.
- Then simply update your extensions through the IPT.
- Sorry, not the easiest work around, but might get you able to  
demonstrate how you can start to build your community without waiting  
for the sandbox repository.

Best wishes,

Tim

>
>
> From: Holetschek, Jörg [mailto:j.holetschek at bgbm.org]
> To: 'Mickael Graf' [mailto:mickael.graf at nrm.se], "\"Markus Döring  
> (GBIF)\"" [mailto:mdoering at gbif.org]
> Cc: ipt at lists.gbif.org [mailto:ipt at lists.gbif.org]
> Sent: Tue, 12 May 2009 13:55:36 +0200
> Subject: Re: [IPT] IPT connection problem
>
> Dear Mickael,
>
> just a small hint... in a former version I also had some problems  
> with SQL connections:
> http://code.google.com/p/gbif-providertoolkit/issues/detail?id=121
>
> Maybe try to restart tomcat to make sure it's not the same problem.
>
> Just an idea,
> Jörg
>
> -----Ursprüngliche Nachricht-----
> Von: ipt-bounces at lists.gbif.org [mailto:ipt-bounces at lists.gbif.org]Im
> Auftrag von Mickael Graf
> Gesendet: Dienstag, 12. Mai 2009 13:28
> An: "Markus Döring (GBIF)"
> Cc: ipt at lists.gbif.org
> Betreff: Re: [IPT] IPT connection problem
>
>
> Markus,
>
> I undeployed RC1 and deployed RC2 and it creates a logfile ipt.log.
> But it doesn't log any error at all related to the connection problem.
>
> BTW, I never wrote it before but the message is "No Database  
> connected.
> Please adjust connection parameters to use SQL sources"
>
> I send you the logfile in case of there is something useful in it.
>
> Cheers
> Mickaël
>
> On Tue, 2009-05-12 at 11:47 +0200, "Markus Döring (GBIF)" wrote:
> > Mickael,
> > the latest IPT war snapshot can be found here:
> >
> > ftp://ftp.gbif.org/projects/ipt/downloads/ipt-1.0RC2-SNAPSHOT.war
> >
> > This version logs connection problems and also uses in addition to
> > tomcat logging an ipt.log file inside the data/logging dir.
> > It also shows a simple message if you configure a bad connection in
> > the manager UI.
> > If you have time, please use this to find out more about your mysql
> > conenction problem.
> >
> > thanks,
> > Markus
> >
> >
> >
> > On May 12, 2009, at 10:17 AM, Markus Döring (GBIF) wrote:
> >
> > > Mickael,
> > > I looked at the source again and the IPT really doesn't log any
> > > errors when changing the db connection.
> > > This is obviously not very helpful, so I've updated the code  
> already
> > > to do so. I will upload a new war file today, so if you like you  
> can
> > > try this version and hopefully find the reason for your connection
> > > problem. Will post the links later.
> > >
> > > many thanks,
> > > Markus
> > >
> > >
> > >
> > > On May 11, 2009, at 6:03 PM, Tim Robertson wrote:
> > >
> > >> Hej Mickael,
> > >>
> > >> Can you please post the logs you get when you configure and  
> save the
> > >> database connection?
> > >>
> > >> Many thanks,
> > >>
> > >> Tim
> > >>
> > >>
> > >>
> > >> On 11 May 2009, at 14:36, Mickael Graf wrote:
> > >>
> > >>> Sorry for posting at the wrong place.
> > >>>
> > >>> The database name is correct, and IPT runs on the same server  
> as the
> > >>> mysql database. This database works perfectly with our TAPIRLink
> > >>> provider.
> > >>>
> > >>> The MySQL server version is 5.0.45 and Connector/J has version
> > >>> 5.1.7. It
> > >>> has been tested against Java 1.6.0 (OpenJDK) and against Sun  
> Java 6
> > >>> Update 12. None of this worked.
> > >>>
> > >>>
> > >>> Cheers,
> > >>> Mickaël
> > >>>
> > >>>
> > >>> On Mon, 2009-05-11 at 10:49 +0200, Tim Robertson wrote:
> > >>>> Hi Mickael,
> > >>>>
> > >>>>
> > >>>> Please always post questions to the list, to help us keep an  
> FAQ up
> > >>>> to
> > >>>> date and allow for others to search etc.
> > >>>>
> > >>>>
> > >>>> I have just tested it myself with the following:
> > >>>>
> > >>>>
> > >>>> Database connection URL: jdbc:mysql://localhost:3306/portal
> > >>>> Database User: tim
> > >>>> Database Password: password
> > >>>>
> > >>>>
> > >>>> and it worked... so, to get started debugging your issue may I
> > >>>> please
> > >>>> ask some basic questions:
> > >>>>
> > >>>>
> > >>>> - You wrote "jdbc:mysql://localhost:3306/databasename" - is  
> your
> > >>>> database name correct?
> > >>>> - You are running the IPT on the same machine as the database?
> > >>>> - You are using mysql?
> > >>>>
> > >>>>
> > >>>> Cheers,
> > >>>>
> > >>>>
> > >>>> Tim
> > >>>>
> > >>>>
> > >>>>
> > >>>> On 11 May 2009, at 10:26, Mickael Graf wrote:
> > >>>>
> > >>>>> Hi Tim,
> > >>>>>
> > >>>>> I'm trying to create a resource in IPT but I encounter a  
> problem
> > >>>>> while
> > >>>>> creating the link to the database: in "Source Data" it is  
> written
> > >>>>> under
> > >>>>> "SQL Data Sources" I have the message "No Database connected.
> > >>>>> Please
> > >>>>> adjust connection parameters to use SQL sources" while it  
> keeps my
> > >>>>> settings correctly. I hope I wrote the jdbc string well:
> > >>>>> jdbc:mysql://localhost:3306/databasename.
> > >>>>>
> > >>>>> I surprised because I am using the same parameters as with
> > >>>>> TAPIRLink
> > >>>>> in
> > >>>>> which I don't have any problem. I don't think I should make  
> any
> > >>>>> changes
> > >>>>> in my grants on my database.
> > >>>>>
> > >>>>> Cheers,
> > >>>>> Mickaël
> > >>>>>
> > >>>>> --
> > >>>>> ---------------------------------
> > >>>>> Mickaël Graf
> > >>>>> Database developper, GBIF Sweden - http://www.gbif.se
> > >>>>> tel: +46 8 5195 4045
> > >>>>> mailto:mickael.graf at nrm.se
> > >>>>>
> > >>>>> Swedish Museum of Natural History - http://www.nrm.se
> > >>>>> Box 50007
> > >>>>> SE-104 05 Stockholm
> > >>>>> Sweden
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>> --
> > >>> ---------------------------------
> > >>> Mickaël Graf
> > >>> Database developper, GBIF Sweden - http://www.gbif.se
> > >>> tel: +46 8 5195 4045
> > >>> mailto:mickael.graf at nrm.se
> > >>>
> > >>> Swedish Museum of Natural History - http://www.nrm.se
> > >>> Box 50007
> > >>> SE-104 05 Stockholm
> > >>> Sweden
> > >>>
> > >>>
> > >>
> > >> _______________________________________________
> > >> IPT mailing list
> > >> IPT at lists.gbif.org
> > >> http://lists.gbif.org/mailman/listinfo/ipt
> > >>
> > >
> >
> --
> ---------------------------------
> Mickaël Graf
> Database developper, GBIF Sweden - http://www.gbif.se
> tel: +46 8 5195 4045
> mailto:mickael.graf at nrm.se
>
> Swedish Museum of Natural History - http://www.nrm.se
> Box 50007
> SE-104 05 Stockholm
> Sweden
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